Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07
Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bact...
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ftmdpi:oai:mdpi.com:/1422-0067/21/24/9363/ 2023-08-20T04:00:54+02:00 Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad agris 2020-12-09 application/pdf https://doi.org/10.3390/ijms21249363 EN eng Multidisciplinary Digital Publishing Institute Molecular Genetics and Genomics https://dx.doi.org/10.3390/ijms21249363 https://creativecommons.org/licenses/by/4.0/ International Journal of Molecular Sciences; Volume 21; Issue 24; Pages: 9363 Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway Text 2020 ftmdpi https://doi.org/10.3390/ijms21249363 2023-08-01T00:37:34Z Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica. Text Antarc* Antarctic Antarctica King George Island South Shetland Islands MDPI Open Access Publishing Antarctic King George Island South Shetland Islands International Journal of Molecular Sciences 21 24 9363 |
institution |
Open Polar |
collection |
MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway |
spellingShingle |
Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
topic_facet |
Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway |
description |
Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica. |
format |
Text |
author |
Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad |
author_facet |
Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad |
author_sort |
Gillian Li Yin Lee |
title |
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
title_short |
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
title_full |
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
title_fullStr |
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
title_full_unstemmed |
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
title_sort |
statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, rhodococcus sp. strain aq5-07 |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2020 |
url |
https://doi.org/10.3390/ijms21249363 |
op_coverage |
agris |
geographic |
Antarctic King George Island South Shetland Islands |
geographic_facet |
Antarctic King George Island South Shetland Islands |
genre |
Antarc* Antarctic Antarctica King George Island South Shetland Islands |
genre_facet |
Antarc* Antarctic Antarctica King George Island South Shetland Islands |
op_source |
International Journal of Molecular Sciences; Volume 21; Issue 24; Pages: 9363 |
op_relation |
Molecular Genetics and Genomics https://dx.doi.org/10.3390/ijms21249363 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/ijms21249363 |
container_title |
International Journal of Molecular Sciences |
container_volume |
21 |
container_issue |
24 |
container_start_page |
9363 |
_version_ |
1774721178160594944 |